The astounding success made by artificial intelligence (AI) in healthcare and other fields proves that AI can achieve human-like performance. However, success always comes with challenges. Deep learning algorithms are data-dependent and require large datasets for training. The lack of data in the medical imaging field creates a bottleneck for the application of deep learning to medical image analysis. Medical image acquisition, annotation, and analysis are costly, and their usage is constrained by ethical restrictions. They also require many resources, such as human expertise and funding. That makes it difficult for non-medical researchers to have access to useful and large medical data. Thus, as comprehensive as possible, this paper provides a collection of medical image datasets with their associated challenges for deep learning research. We have collected information of around three hundred datasets and challenges mainly reported between 2013 and 2020 and categorized them into four categories: head & neck, chest & abdomen, pathology & blood, and ``others''. Our paper has three purposes: 1) to provide a most up to date and complete list that can be used as a universal reference to easily find the datasets for clinical image analysis, 2) to guide researchers on the methodology to test and evaluate their methods' performance and robustness on relevant datasets, 3) to provide a ``route'' to relevant algorithms for the relevant medical topics, and challenge leaderboards.
Recently, visual Transformer (ViT) and its following works abandon the convolution and exploit the self-attention operation, attaining a comparable or even higher accuracy than CNNs. More recently, MLP-Mixer abandons both the convolution and the self-attention operation, proposing an architecture containing only MLP layers. To achieve cross-patch communications, it devises an additional token-mixing MLP besides the channel-mixing MLP. It achieves promising results when training on an extremely large-scale dataset. But it cannot achieve as outstanding performance as its CNN and ViT counterparts when training on medium-scale datasets such as ImageNet1K and ImageNet21K. The performance drop of MLP-Mixer motivates us to rethink the token-mixing MLP. We discover that the token-mixing MLP is a variant of the depthwise convolution with a global reception field and spatial-specific configuration. But the global reception field and the spatial-specific property make token-mixing MLP prone to over-fitting. In this paper, we propose a novel pure MLP architecture, spatial-shift MLP (S$^2$-MLP). Different from MLP-Mixer, our S$^2$-MLP only contains channel-mixing MLP. We utilize a spatial-shift operation for communications between patches. It has a local reception field and is spatial-agnostic. It is parameter-free and efficient for computation. The proposed S$^2$-MLP attains higher recognition accuracy than MLP-Mixer when training on ImageNet-1K dataset. Meanwhile, S$^2$-MLP accomplishes as excellent performance as ViT on ImageNet-1K dataset with considerably simpler architecture and fewer FLOPs and parameters.
The idea of Innovation Search, which was initially proposed for data clustering, was recently used for outlier detection. In the application of Innovation Search for outlier detection, the directions of innovation were utilized to measure the innovation of the data points. We study the Innovation Values computed by the Innovation Search algorithm under a quadratic cost function and it is proved that Innovation Values with the new cost function are equivalent to Leverage Scores. This interesting connection is utilized to establish several theoretical guarantees for a Leverage Score based robust PCA method and to design a new robust PCA method. The theoretical results include performance guarantees with different models for the distribution of outliers and the distribution of inliers. In addition, we demonstrate the robustness of the algorithms against the presence of noise. The numerical and theoretical studies indicate that while the presented approach is fast and closed-form, it can outperform most of the existing algorithms.
Low-dose computed tomography (CT) allows the reduction of radiation risk in clinical applications at the expense of image quality, which deteriorates the diagnosis accuracy of radiologists. In this work, we present a High-Quality Imaging network (HQINet) for the CT image reconstruction from Low-dose computed tomography (CT) acquisitions. HQINet was a convolutional encoder-decoder architecture, where the encoder was used to extract spatial and temporal information from three contiguous slices while the decoder was used to recover the spacial information of the middle slice. We provide experimental results on the real projection data from low-dose CT Image and Projection Data (LDCT-and-Projection-data), demonstrating that the proposed approach yielded a notable improvement of the performance in terms of image quality, with a rise of 5.5dB in terms of peak signal-to-noise ratio (PSNR) and 0.29 in terms of mutual information (MI).
The method of random projection (RP) is the standard technique in machine learning and many other areas, for dimensionality reduction, approximate near neighbor search, compressed sensing, etc. Basically, RP provides a simple and effective scheme for approximating pairwise inner products and Euclidean distances in massive data. Closely related to RP, the method of random Fourier features (RFF) has also become popular, for approximating the Gaussian kernel. RFF applies a specific nonlinear transformation on the projected data from random projections. In practice, using the (nonlinear) Gaussian kernel often leads to better performance than the linear kernel (inner product), partly due to the tuning parameter $(\gamma)$ introduced in the Gaussian kernel. Recently, there has been a surge of interest in studying properties of RFF. After random projections, quantization is an important step for efficient data storage, computation, and transmission. Quantization for RP has also been extensive studied in the literature. In this paper, we focus on developing quantization algorithms for RFF. The task is in a sense challenging due to the tuning parameter $\gamma$ in the Gaussian kernel. For example, the quantizer and the quantized data might be tied to each specific tuning parameter $\gamma$. Our contribution begins with an interesting discovery, that the marginal distribution of RFF is actually free of the Gaussian kernel parameter $\gamma$. This small finding significantly simplifies the design of the Lloyd-Max (LM) quantization scheme for RFF in that there would be only one LM quantizer for RFF (regardless of $\gamma$). We also develop a variant named LM$^2$-RFF quantizer, which in certain cases is more accurate. Experiments confirm that the proposed quantization schemes perform well.
Due to the intractable partition function, training energy-based models (EBMs) by maximum likelihood requires Markov chain Monte Carlo (MCMC) sampling to approximate the gradient of the Kullback-Leibler divergence between data and model distributions. However, it is non-trivial to sample from an EBM because of the difficulty of mixing between modes. In this paper, we propose to learn a variational auto-encoder (VAE) to initialize the finite-step MCMC, such as Langevin dynamics that is derived from the energy function, for efficient amortized sampling of the EBM. With these amortized MCMC samples, the EBM can be trained by maximum likelihood, which follows an "analysis by synthesis" scheme; while the variational auto-encoder learns from these MCMC samples via variational Bayes. We call this joint training algorithm the variational MCMC teaching, in which the VAE chases the EBM toward data distribution. We interpret the learning algorithm as a dynamic alternating projection in the context of information geometry. Our proposed models can generate samples comparable to GANs and EBMs. Additionally, we demonstrate that our models can learn effective probabilistic distribution toward supervised conditional learning experiments.
Given a set $\mathcal{C}=\{C_i\}_{i=1}^m$ of square matrices, the matrix blind joint block diagonalization problem (BJBDP) is to find a full column rank matrix $A$ such that $C_i=A\Sigma_iA^\text{T}$ for all $i$, where $\Sigma_i$'s are all block diagonal matrices with as many diagonal blocks as possible. The BJBDP plays an important role in independent subspace analysis (ISA). This paper considers the identification problem for BJBDP, that is, under what conditions and by what means, we can identify the diagonalizer $A$ and the block diagonal structure of $\Sigma_i$, especially when there is noise in $C_i$'s. In this paper, we propose a ``bi-block diagonalization'' method to solve BJBDP, and establish sufficient conditions under which the method is able to accomplish the task. Numerical simulations validate our theoretical results. To the best of the authors' knowledge, existing numerical methods for BJBDP have no theoretical guarantees for the identification of the exact solution, whereas our method does.
In recent years, low-rank tensor completion (LRTC) has received considerable attention due to its applications in image/video inpainting, hyperspectral data recovery, etc. With different notions of tensor rank (e.g., CP, Tucker, tensor train/ring, etc.), various optimization based numerical methods are proposed to LRTC. However, tensor network based methods have not been proposed yet. In this paper, we propose to solve LRTC via tensor networks with a Tucker wrapper. Here by "Tucker wrapper" we mean that the outermost factor matrices of the tensor network are all orthonormal. We formulate LRTC as a problem of solving a system of nonlinear equations, rather than a constrained optimization problem. A two-level alternative least square method is then employed to update the unknown factors. The computation of the method is dominated by tensor matrix multiplications and can be efficiently performed. Also, under proper assumptions, it is shown that with high probability, the method converges to the exact solution at a linear rate. Numerical simulations show that the proposed algorithm is comparable with state-of-the-art methods.
Neural network classifiers are vulnerable to data poisoning attacks, as attackers can degrade or even manipulate their predictions thorough poisoning only a few training samples. However, the robustness of heuristic defenses is hard to measure. Random selection based defenses can achieve certified robustness by averaging the classifiers' predictions on the sub-datasets sampled from the training set. This paper proposes a framework of random selection based certified defenses against data poisoning attacks. Specifically, we prove that the random selection schemes that satisfy certain conditions are robust against data poisoning attacks. We also derive the analytical form of the certified radius for the qualified random selection schemes. The certified radius of bagging derived by our framework is tighter than the previous work. Our framework allows users to improve robustness by leveraging prior knowledge about the training set and the poisoning model. Given higher level of prior knowledge, we can achieve higher certified accuracy both theoretically and practically. According to the experiments on three benchmark datasets: MNIST 1/7, MNIST, and CIFAR-10, our method outperforms the state-of-the-art.